Metabolite Profiling Experiments

The GC-MS metabolite profiling experiments given below are made
publicly available to get feedback from the community. The relative metabolite concentrations
are normalised according to fresh weight (or comparable quantitative data, such
as volume, cell count, etc.) and internal standards (e.g. ribotol). Although these
details are accessible within the GMD, they are not made available on the web site
so far. For these details please refer to the publication. As it is our intention
to increase the breadth GMD’s experiment repository in terms of organisms, organs
and stresses, we actively work on cross experiment normalisation and thus, profile
data and data representation might change in the future without any further notice.
For maximal quality assessment, all experiments are described using the XEML framework (see tree below), while the
GC-MS chromatograms are processed using the TagFinder software.

metabolic changes during developmental senescence: a case study on Arabidopsis thaliana (single leaves)contact: kopka@mpimp-golm.mpg.dedescription: Developmental senescence is a coordinated physiological process in plants and is critical for nutrient redistribution from senescing leaves to newly formed sink organs, including young leaves and developing seeds. Progress has been made concerning the genes involved and the regulatory networks controlling senescence. The resulting complex metabolome changes during senescence have not been investigated in detail yet. Therefore, we conducted a comprehensive profiling of metabolites, including pigments, lipids, sugars, amino acids, organic acids, nutrient ions, and secondary metabolites, and determined approximately 260 metabolites at distinct stages in leaves and siliques during senescence in Arabidopsis (Arabidopsis thaliana). This provided an extensive catalog of metabolites and their spatiotemporal cobehavior with progressing senescence. Comparison with silique data provides clues to source-sink relations. Furthermore, we analyzed the metabolite distribution within single leaves along the basipetal sink-source transition trajectory during senescence. Ceramides, lysolipids, aromatic amino acids, branched chain amino acids, and stress-induced amino acids accumulated, and an imbalance of asparagine/aspartate, glutamate/glutamine, and nutrient ions in the tip region of leaves was detected. Furthermore, the spatiotemporal distribution of tricarboxylic acid cycle intermediates was already changed in the presenescent leaves, and glucosinolates, raffinose, and galactinol accumulated in the base region of leaves with preceding senescence. These results are discussed in the context of current models of the metabolic shifts occurring during developmental and environmentally induced senescence. As senescence processes are correlated to crop yield, the metabolome data and the approach provided here can serve as a blueprint for the analysis of traits and conditions linking crop yield and senescence. start date: 1900-01-01experiment Id:
542eb5ee-9f53-4ec0-bf81-92c67e95625flinks: metabolite profileMapMan pathwayXEML experimental descriptionISA-Tab export

This tree schematises the experimental design
of a single metabolite profiling experiment with the x-axis representing the time
scale. Branches of the tree are used to describe the plant’s environmental condition.
Recorded environmental conditions are either given to describe the general experimental
setup and to support cross experiment comparisons, or to indicate the specific stress
type. A “salt stress experiment” is described using different salt concentrations.
Clicking the nodes of the tree, quantitative environmental conditions (e.g. temperature,
salt concentrations, humidity, etc.) describing the plant’s environment can be inspected
in the right table. Unfortunately, due to the limitations of the current html based
visualisation, the scaling of the tree's branches is not proportional to the real
length of time. Green tagged observation points (OP) represent sampling time points.
Results in the data analysis (see heat map or MapMan links in table on top) correspond
to these observation points. Please note that observation point names (OP1, OP2,
etc.) do not relate to each other. Instead, use the description of the observation
points to identify potential candidates for cross experiment profile comparison.